Visualizing molecular self-assembly has emerged as one of the great challenges in modern biophysics, related to phenomena ranging from nanotechnology applications and bio inspired material science to the formation of molecular machineries in living cells. In particular, an example of biomolecular self-assembly that gives rise to an important class of macromolecular structures is the formation of protein aggregates the so-called amyloid fibrils. Super-resolution microscopy has emerged as a powerful and non-invasive tool for the study of such processes both in vitro, but also as they occur in live cells. In this talk I will discuss the main principles of the super resolution microscopy technique based on single molecule localization. I will then present the application of one such technique, the direct stochastic optical reconstruction microscopy (dSTORM), to determine the morphology of amyloid proteins as it evolves over time in vitro, but also as it emerges in a complex cellular environment. Using two-colour dSTORM we have shown that there is heterogeneity in the growth rates of individual amyloid fibrils which can be attributed to structural polymorphism. In neuronal cells, we have shown that exogenously added α-synuclein seed fibrils primarily elongate by the endogenous α-synuclein, naturally present in neurons. In contrast, exogenously added monomeric α-synuclein induces nucleation of the endogenous protein and leads to apoptosis. The latter is rescued by the addition of seed fibrils, suggesting a neuroprotective role of fibrillar species. The visualization of these effects at the nanoscale opens up new avenues for understanding the links between α-synuclein aggregation and neuronal toxicity.